Increase in anthropogenic pCO2 alters seawater chemistry and could lead to reduced calcification or skeleton dissolution of calcifiers and thereby weaken coral-reef structure. Studies have suggested that the complex and diverse responses in stony coral growth and calcification, as a result of elevated pCO2, can be explained by the extent to which their soft tissues cover the underlying skeleton. This study compared the effects of decreased pH on the microstructural features of both in hospite (within the colony) and isolated sclerites (in the absence of tissue protection) of the zooxanthellate reef-dwelling octocoral Ovabunda macrospiculata. Colonies and isolated sclerites were maintained under normal (8.2) and reduced (7.6 and 7.3) pH conditions for up to 42 days. Both in hospite and isolated sclerites were then examined under SEM and ESEM microscopy in order to detect any microstructural changes. No differences were found in the microstructure of the in hospite sclerites between the control and the pH treatments. In stark contrast, the isolated sclerites revealed dissolution damage related to the acidity of the water. These findings suggest a protective role of the octocoral tissue against adverse pH conditions, thus maintaining them unharmed at high pCO2. In light of the competition for space with the less resilient reef calcifiers, octocorals may thus have a significant advantage under greater than normal acidic conditions.